graftM create error about graftm HOT 6 OPEN

________________________________ From: Aditya Bandla <[email protected]> Sent: Tuesday, May 12, 2020 6:12:41 AM To: geronimp/graftM <[email protected]> Cc: Subscribed <[email protected]> Subject: [geronimp/graftM] graftM create error (#265) I am trying to build a graftM package for the rpsB gene from the GTDB r89 species-level genomes. I downloaded the unaligned bacterial & archaeal marker gene sequences & concatenated them (i.e. TIGR01011.fna & TIGR01012.fna). Modified the taxonomy files to match the contig headers in the sequence fasta. Next, I attempted to create the packages by graftM create --sequences rpsB_bac_arc.fna --taxonomy rpsB_bac_arc_taxonomy.tsv --threads 24 But I ran into this error Traceback (most recent call last): File "/home/projects/11001755/miniconda3/envs/singlem/bin/graftM", line 415, in <module> Run(args).main() File "/home/projects/11001755/miniconda3/envs/singlem/lib/python3.6/site-packages/graftm/run.py", line 681, in main threads = self.args.threads File "/home/projects/11001755/miniconda3/envs/singlem/lib/python3.6/site-packages/graftm/create.py", line 636, in main align_hmm, output_alignment, threads) File "/home/projects/11001755/miniconda3/envs/singlem/lib/python3.6/site-packages/graftm/create.py", line 454, in _align_and_create_hmm output_alignment) File "/home/projects/11001755/miniconda3/envs/singlem/lib/python3.6/site-packages/graftm/create.py", line 143, in _get_hmm_from_alignment output = extern.run(cmd) File "/home/projects/11001755/miniconda3/envs/singlem/lib/python3.6/site-packages/extern/__init__.py", line 41, in run raise ExternCalledProcessError(process, command) extern.ExternCalledProcessError: Command hmmbuild -O /dev/stdout -o /dev/stderr '/var/tmp/pbs.71118.wlm01/graftmbcgozapa_align.hmm' '/var/tmp/pbs.71118.wlm01/graftm3k540rg3.aln.faa' returned non-zero exit status 7. STDERR was: b'Alignment input parse error:\n sequence GCF_002135345.1 has alen 5348; expected 25270\n while reading aligned FASTA file /var/tmp/pbs.71118.wlm01/graftm3k540rg3.aln.faa\n at or near line 7171633\n# hmmbuild :: profile HMM construction from multiple sequence alignments\n# HMMER 3.3 (Nov 2019); http://hmmer.org/\n# Copyright (C) 2019 Howard Hughes Medical Institute.\n# Freely distributed under the BSD open source license.\n# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n# input alignment file: /var/tmp/pbs.71118.wlm01/graftm3k540rg3.aln.faa\n# output HMM file: /var/tmp/pbs.71118.wlm01/graftmbcgozapa_align.hmm\n# output directed to file: /dev/stderr\n# processed alignment resaved to: /dev/stdout\n# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -\n\n# idx name nseq alen mlen W eff_nseq re/pos description\n#---- -------------------- ----- ----- ----- ----- -------- ------ -----------\n'STDOUT was: b'' — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#265>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AAADX5COUOOIOKX6UBGOBEDRRBL3TANCNFSM4M6G6JCQ>.